Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of the protein targets of a small molecule

ABSTRACT: Mass spectrometry-based chemical proteomic approaches using limited proteolysis for analysis of the interactions between a small molecule and its protein target(s). DARTS (Drug Affinity Responsive Target Stability) has been used in this study on Hela cell lysate. Ubiquitin carboxyl-terminal hydrolase 5 (USP5) was identified as one of the targets of the studied small molecule.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Uterine Cervix

SUBMITTER: Gilda D'Urso

LAB HEAD: Agostino Casapullo

PROVIDER: PXD048098 | Pride | 2024-01-15

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	GE_D4_B1_1a500_100um.raw	Raw
	GE_D4_B1_1a500_10uM.raw	Raw
	GE_D4_B1_1a500_1uM.msf	Msf
	GE_D4_B1_1a500_1uM.msfView	Msf
	GE_D4_B1_1a500_1uM.raw	Raw

Items per page:

1 - 5 of 63

Similar Datasets

Fatty Acid Synthase as Interacting Anticancer Target of the Terpenoid Myrianthic Acid disclosed by MS-Based Proteomics Approaches

Project description:This research focuses on the target deconvolution of the natural compound myrianthic acid, a triterpenoid characterized by an ursane skeleton isolated from the roots of Myrianthus arboreus and from Oenothera maritima Nutt. (Onagraceae), using MS-based chemical proteomic techniques. Application of Drug Affinity Responsive Target Stability (DARTS) and targeted-Limited Proteolysis coupled to Mass Spectrometry (t-LiP-MS) led to the identification of the enzyme fatty acid synthase (FAS) as an interesting macromolecular counterpart of myrianthic acid. This result, confirmed by comparison with the natural triteprenoid ursolic acid, was thoroughly investigated and validated in silico by molecular docking, which gave a precise picture of the interactions in the MA/FAS complex. Moreover, in vitro biological assays showcased the inhibitory activity of myrianthic acid against the FAS enzyme, most likely related to its antiproliferative activity towards tumor cells. Given the sig-nificance of FAS in specific pathologies, especially cancer, the myrianthic acid structural moieties could serve as a promising reference point to start a potential development of innovative ap-proaches in therapy.

2024-06-23 | PXD052306 | Pride

Unveiling Adaptive Molecular Mechanisms Through Comparative Proteomics of Potato Cell Responses to Abrupt and Gradual Water Deficits

Project description:Osmotic stress, such as drought and salinity, impairs plant growth, productivity, and food quality. Plants cope with these stresses by modulating biological processes and molecular mechanisms based on the stress intensity and duration. Understanding how plants respond and adapt at the molecular level is crucial for developing tolerant genotypes capable of surviving and produce in harsh conditions. The cultivated potato Solanum tuberosum is the most important non-grain crop worldwide and is often considered water deficit sensitive, thus necessitating efforts to enhance their resilience. Previously, we established a reliable in vitro model using potato suspension cells to simulate sudden (shock) or gradual adaptation to water deficit. Our previous researches revealed distinct cellular and molecular responses between shocked and adapted cells. In this study, we utilized mass spectrometry-based proteomics to examine protein expression in order to capture novel functional information and identify regulatory networks during gradual adaptation compared to abrupt water stress. Remarkably, both adapted and shocked conditions triggered significant alterations in protein expression related to various metabolic pathways, including carbon metabolism, osmotic regulation, and antioxidant defense. However, adapted cells exhibited increased levels of proteins associated with fatty acid biosynthesis and metabolism, underscoring the importance of fatty acids in regulating potato cell adaptation to water deficit. Furthermore, we identified proteins involved in transcriptional and translational machinery, as well as chromatin organization, which were specifically expressed in adapted cells. This suggests a pivotal role for epigenetic changes, warranting further investigation. Importantly, our findings present a valuable list of candidate proteins for future functional analysis to elucidate their roles in plant stress response and adaptive mechanisms.

2024-12-06 | PXD050665 | Pride

USP5 stabilizes YTHDF1 to control cancer immune surveillance through mTORC1-mediated phosphorylation

Project description:N6-methyladenosine (m6A) binding protein YTHDF1 is frequently upregulated in various cancers and its depletion enhances the efficacy of immune checkpoint blockade (ICB) therapy. This study reveals that USP5 interacts with YTHDF1, preventing its K11-linked polyubiquitination, thereby stabilizing YTHDF1 and promoting its oncogenic properties. In response to insulin, mTORC1 phosphorylates USP5, facilitating its dimerization and subsequent binding to YTHDF1, while the CUL7-FBXW8 complex promotes its degradation. Notably, YTHDF1 or USP5 deficiency increases PD-L1 expression and impairs immune response gene expression, contributing to immune evasion. Combining USP5 inhibitors with anti-PD-1 therapy enhances antitumor T-cell immunity and improves tumor regression in mouse models. Thus, USP5 may serve as a biomarker for stratifying patients for anti-PD-1 therapy, suggesting a novel strategy of combining USP5 inhibition with PD-(L)1 blockade to enhance cancer treatment efficacy.

2024-12-05 | GSE278264 | GEO

Drug Affinity Responsive Target Stability unveils Filamins as biological targets for Artemetin, an anti-cancer flavonoid.

Project description:Artemetin is a valuable 5-hydroxy-3,6,7,3',4'-pentamethoxyflavone found in many different medicinal plants with a very good oral bioavailability and drug-likeness values endowed with numerous bioactivities such as anti-inflammatory and anti-cancer ones. Here, a multi-disciplinary strategy has been developed and applied for identifying Artemetin target(s) to fully address its mechanism of action, based on drug affinity response target stability and targeted limited proteolysis. Both approaches point to the identification of Filamins A and B as major Artemetin targets in HeLa cell lysates, giving also detailed insights into the ligand/proteins interaction sites. Interestingly, also the 8-prenyl-Artemetin, which is a more permeable semisynthetic analog, directly interacts with Filamin A and B. Both compounds alter filamins conformation in living HeLa cells with an effect on cytoskeleton disassembly and on the disorganization of the F-actin filaments, mediated by the dissociation of filamins. Both the natural compound and its derivative are able to block cell migration, expectantly acting on tumor metastasis’s occurrence and development.

2022-10-14 | PXD034776 | Pride

Identification of Cannabidiol interactome in K562 cells

Project description:Cannabidiol (CBD) showed antiproliferative activity and induction of apoptosis in chronic myelogenous leukaemia cancer cells (K562 cells). A consolidated DARTS (Drug Affinity Response Target Stability) and t-LIP-MRM (targeted- Limited Proteolysis-Multiple Reaction Monitoring Mass spectrometry) platform was applied to unveil the interactome of CBD and to shed light on its mechanism of action. Both approaches point to the identification of DNA topoisomerase 2-alpha (TOP2A) as a major CBD target in K562 cells.

2024-01-26 | PXD036650 | Pride

USP5 stabilizes YTHDF1 to control cancer immune surveillance through mTORC1-mediated phosphorylation

Project description:The N6-methyladenosine (m6A) binding protein YTHDF1 emerges as a frequently upregulated oncogene across various cancer types. Its depletion significantly improves the efficacy of cancer immune checkpoint blockade (ICB) treatment. A comprehensive understanding of the molecular mechanisms governing YTHDF1 protein stability is pivotal for enhancing clinical response rates and the effectiveness of ICB in cancer patients. Here, we report that USP5 interacts with YTHDF1, removing K11-linked polyubiquitination on multiple lysine residues to stabilize YTHDF1, thereby conferring its oncogenic properties. In response to insulin, mTORC1 phosphorylates USP5 at S149, promoting its dimerization. Dimerized USP5 then binds to YTHDF1, preventing its degradation. Conversely, the CUL7-FBXW8 E3 ubiquitin ligase promotes K11-linked polyubiquitination and degradation of YTHDF1. USP5 and FBXW8 thus regulate YTHDF1 ubiquitylation at defined residues through mutually exclusive interactions and opposing activities. Furthermore, deficiency in YTHDF1 or USP5 enhances PD-L1 expression and compromises the expression of multiple immune response-related genes, fostering cancer immune evasion. Remarkably, combining USP5 inhibitor treatment with anti-PD-1 immunotherapy reprograms the antitumor T-cell immunity environment, leading to enhanced tumor regression and markedly improved overall survival rates in mouse tumor models. Therefore, in hepatocellular carcinoma and lung cancer patients, USP5 may serve as a promising biomarker for stratifying individuals for anti-PD-1 therapy. Our findings reveal a ubiquitination-dependent regulation of YTHDF1 protein stability influencing immune response gene expression, suggesting USP5 inhibition combined with PD-(L)1 blockade as a novel and promising strategy for cancer treatment.

2024-12-11 | GSE255922 | GEO

Inhibition of USP5 offers potential targeted therapeutic strategies for t(8;21) AML through ubiquitin-mediated degradation of AML1-ETO

Project description:The AML1-ETO (AE) fusion protein is a key target for treating t(8;21) acute myeloid leukemia (AML). In this investigation, we identified ubiquitin-specific protease 5 (USP5) as the deubiquitinating enzyme of AE. USP5 knockdown decreased AML cell growth and induced differentiation both in vitro and in vivo. Additionally, we developed a high-throughput screening (HTS) method and identified a potent, selective USP5 inhibitor, WCY-8-67. This lead compound was identified as a selective USP5 inhibitor via targeting the ubiquitin-associated domain 2 (UBA2) region, and it also induced aggregation and precipitation of the target protein, leading to USP5 dysfunction. WCY-8-67 was exhibited excellent in vivo bioavailability and tolerability, and it effectively inhibited the growth of t(8;21) AML cell lines and the primary AML cells in animal models. Notably, in the patient-derived xenograft (PDX) model, this compound, when combined with 5-Azacytidine (5-Aza), demonstrated good safety and significant synergistic therapeutic effects. This study presented promising targeted therapeutic possibilities for the treatment of t(8;21) AML.

2025-09-02 | GSE306372 | GEO

Transcription profiling by array to investigate USP5 knock out in cardiomycytes

Project description:The experiment compares cardiomyocytes isolated from Control and USP5 KO mice 15 days after deletion by tamoxifen administration.

2024-12-14 | E-MTAB-6839 | biostudies-arrayexpress

WT/Usp5-MKO PM cells were stimulated with LPS or not

Project description:Test transcripts in mock and LPS stimulated PM cells from WT or Usp5 myeloid knockout mice

2024-08-11 | GSE240642 | GEO

WT or Usp5 knockout (KO) PMs were infected with HSV-1 or not

Project description:Transcriptome profiling analysis to study deubiquitinase gene expression levels in HSV-1 infected WT or Usp5 KO PMs

2024-06-01 | GSE233795 | GEO